Biopunk: DIY Scientists Hack the Software of Life

Marcus Wohlsen has covered startup culture, the maker scene, and the marijuana industry as a reporter in the San Francisco bureau of The Associated Press. His first book, Biopunk: DIY Scientists Hack the Software of Life, was published this week by Current. I asked him to contribute a few pieces about the biotech underground to run on Boing Boing. Here's the first one.
biopunk.jpg HACK/OPEN: DNA, DIY and the right to do

The first time I met Meredith Patterson, she lived in a weird old apartment building plunked down in Pacific Heights, just below where the street rose to an epic view of San Francisco Bay and the Golden Gate. Christmas trees glowed in the windows of the mansions nearby. Inside, the walk-up's arches, doors and sconces gave off a cheesy 1940s Hollywood "Moorish" vibe. I didn't know what to expect a DNA hacker's lair to look like, because I had no idea who would want to hang out at home tinkering with genes in the first place.

But I should have guessed Meredith. If she hadn't existed, screenwriters would have invented her. Tattoos. Gauged ears. A smoker. Black t-shirt. Black leather trench coat. Boxes of disemboweled electronics littering the apartment. Shelves sagging with heavy tomes of sci-fi, coding manuals, linguistics texts and histories of cryptography. The consummate hacker chick before the English-speaking world had ever heard of Lisbeth Salander.

Her wet lab was on the dining room table. The setup included a hot plate, yogurt containers, beakers, dozens of small plastic vials and a jerry-rigged thermal cycler, a kind of glorified crock pot that serves as the essential gene-brewing tool in almost all modern biotech. We spent the next hour or so chatting as she filled tube after tube with a clear liquid that she assured me contained both yogurt bacteria and the jellyfish gene she planned to splice into it. Like hackers of every stripe, she was playing with this stuff because has a compulsive need to tweak. And like so many hackers, she thought her hack could change the world.

As Patterson hunched over the table in late 2008, China was mired in scandal over tainted infant formula that had sickened thousands and killed at least four. The deaths exposed a longstanding practice among Chinese dairy producers of cutting milk powder with melamine, an organic compound commonly used to make plastics. The toxin could fool nutritional tests to make the milk appear to contain more protein than it did. Like heroin dealers, the dairy producers "stepped on" their milk powder to stretch the supply further.

Standard tests for melamine involve mass spectrometers -- cumbersome, expensive, complex pieces of lab equipment useful for testing the food supply at the distribution level or after someone gets sick. Patterson reasoned that this method wouldn't help a Chinese peasant farmer staring down a bottle of formula trying to decide whether to feed her baby. That mother needs immediate results. And those results need to come cheap.

Yogurt is cheap, as are jellyfish. Buy a tub of yogurt at Trader Joe's as Patterson had done and you have a theoretically limitless supply of Lacto bacilli as long as you keep feeding them a little bit of milk sugar. For about $50 from Carolina Biological Supply you can get a high school AP biology kit that contains the jellyfish gene you need to make green fluorescent protein. It was this jellyfish gene Patterson was trying to splice with the yogurt bacteria the night I hung out with her.

The "melaminometer," as Patterson and her collaborators called their hack, ends up sounding oddly simple for a radical feat of genetic engineering. Jack the genes for a melamine-sensitive protein into the yogurt bacteria. Concoct a chemical trigger that sets off the jellyfish gene. Suddenly you have a $1 vial into which the mother in China adds a few drops of formula. If there's melamine, it glows green. Voila: A user-friendly, consumer-grade detector that enables crowdsourced safety monitoring of the world's food supply. Someone call Bill and Melinda Gates.

So why two years later does the melaminometer remain just an idea? From the OpenWetWare wiki tracking the effort: "This project has not moved forward due to inability for synthetic biology labs to scope engineering of a suitable detector as proposed by this design. Thus, this project is currently vaporware, until technology can catch up to the proposed genetic circuit." In other words, the engineering for the last few parts, like so much else in modern biology, is just too damn hard right now.

Which kicks the question back to the apparent absurdity of trying to build a genetically engineered melamine detector in your dining room in the first place. Why not leave the do-it-yourself projects to the coders, the steampunks, the Arduino jocks? The stuff that we know is doable -- and safe?

For Patterson, part of the issue is she believes no company could find adequate profit potential in a project like the melaminometer, aimed at the world's poorest people, which leaves a DIY solution as the only realistic approach. The biotech mainstream doesn't buy it, arguing that the technology just hasn't arrived.

But the issue runs deeper for Patterson, and the growing number of biohackers around the world. Success at this point seems incidental to the ambitious crews setting up community wet labs, trading gel buffer recipes online and getting their open-source DNA replicators funded on Kickstarter. For these groups, as for Patterson, the measure of success is in the doing -- and in claiming the right to do.

"We reject the popular perception that science is only done in million-dollar university, government, or corporate labs; we assert that the right of freedom of inquiry, to do research and pursue understanding under one's own direction, is as fundamental a right as that of free speech or freedom of religion," Patterson writes in A Biopunk Manifesto, a biohacker call-to-arms she wrote last year.

"We have no quarrel with Big Science; we merely recall that Small Science has always been just as critical to the development of the body of human knowledge, and we refuse to see it extinguished." Tomorrow: Safety/Risk

Buy Biopunk: DIY Scientists Hack the Software of Life on Amazon


  1. How does a person afford to set up molecular & cell biology in their own house? I work in a lab at the university I attend and some of the simplest, most essential tools are astronomically expense. Take an 250 unit RNA extraction kit for example. It is required in the vast majority of molecular and genetic research labs to understand the products of modified proteins and monitor gene expression. Without the ability to review the RNA in a treatment, a researcher who transforms the genes of yogurt would have no idea which genes were transformed (specifically targeting genes for transformation is extremely difficult, Arabidopsis researchers have to transform hundreds upon hundreds of plants and painstakingly examine every one to determine if the gene was transformed correctly). If the researcher didn’t know which genes were transformed, then they would have no way of knowing whether their bacteria was “working as intended” (barring testing each bacterial sample on a tainted dairy sample). Oh right, and the 250 unit kit costs about $1000, about $4.00 per trial.

  2. According to the wiki they were actually proposing to look at the melamine breakdown products. The project seems to have been a “flash in the pan” with updates for three months and then… silence.

    I applaud the Patterson concept and look forward to more excerpts from Wohlson’s book. For Biohackers though, please don’t underestimate the difficulty of these sorts of projects.

  3. Oh great – you know how some from the tinfoil hat brigade accuse scientists of creating AIDS? Well jacking with genes on your table in the middle of a crowded city with no protective measures like this might actually eventually cause the creation of a superbug if we’re not careful.

    1. If you’re afraid of what Meredith was doing, you should be absolutely terrified of what the bacteria themselves do, trading genes with each other and absorbing genes from their hosts willy-nilly, thereby running billions of potential homegrown biohacking labs in your own body, every single day. You don’t think bacteria ever infect jellyfish in the wild?

      1. Imagine if somebody took a common pathogen like Streptococcus aeruginosa, tweaked it to be resistant to all sorts of antibiotics normally used to kill it, and then let it loose in a hospital. Would anyone notice?

        1. What you’re talking about is bioterrorism. And it’s like saying that because it’s theoretically possible to write a virus that spreads and destroys data in critical lifesaving systems and infrastructures, therefore nobody should be allowed to write any homebrew software.

          You’re conflating an enormous number people who want to help with a very small handful of theoretical people who may want to hurt. Outlawing the helpers is not going to stop the hurters because the latter are going to operate intentionally and knowingly outside the law. Therefore your argument leads to significant loss of freedom and innovation with no positive effects.

          1. Actually I was kidding; my guess is nobody actually would notice, because those things appear spontaneously. But I mixed up the species name – should’ve been aureofaciens – so that probably ruined it. :(

  4. RNA purification is irrelevant to this type of project. DNA purification is critical, but you don’t need to buy an expensive kit for that (though it does make it faster and more convenient). You can get DNA suitable for transformation or PCR (that’s what the thermal cycler mentioned above is for) with very common reagents. I could get what I need from an average grocery store.

    Things like agar plates are also cheap and easy, and bacterial colonies can easily be screened for your gene of interest using PCR instead of getting fancy. As long as you can cobble together some of the equipment and maybe make your own enzymes, this kind of thing is doable at home.

  5. The brewer’s melaminometer was actually intended as the midpoint of a larger project that’s been shelved for the same reasons. FWIW, Meredith had a whole bunch of other stuff happen to her – from having a sick husband to getting into fights with old sysadmins and the US military.

    Honestly, the point of the melaminometer was to do a little world-saving while making lactobacillis into Meredith’s bitch. What she really wanted to do was develop a human-safe probiotic that could act as a metabolic prosthetic and return vitamin C synthesis to the human body. (Humans & other primates can’t synthesize vitamin C, other mammals can) Curing scurvy is a pretty awesome hack, but it’s hard to do. You don’t want too much being made, or too little, so you need to add a bunch of local intelligence to your synthesizer bugs to keep them from poisoning end-users or anything else they end up in.

  6. This is really cool. There are hundreds of such projects, making simple and low-cost solutions to large problems, which are in the reach of citizen scientists. Often the large science labs don’t think about this sort of process, or only work on it incidentally, since there’s (i) no market for people in developing countries, and (ii) the problems are scientifically already solved (albeit using methods unavailable to much of the developing world).

    Off the top of my head, I’d love to see a simple, low cost test for arsenic, which contaminates drinking water in Bangladesh. Or folks could work on a way to bind the arsenic to reduce its toxicity or make it easy to remove. Current tests are about $4 for a single use (which is dramatically less than even 20 years ago).

    We’re likely going to face a shortage of copper in the next 30 or 40 years. What are good replacement materials? Copper is a good conductor, can we come up with better conductors which are low cost and renewable? Organic conductor research is in its infancy, so much of it would be hard to replicate at home. However it would be interesting to try.

    Plastics can be transformed into a oil-base which can then be re-refined into gasoline. Can this be done cheaply and on a reasonable scale to make local gasoline manufacture possible using discarded plastic?

    I know of no way of verifying that milk is rBST-free other than trusting the supply chain and producer. I’m not sure of the challenges of trying to devise a low-cost test, but it would certainly be an interesting project.

    This is off the top of my head. Of course, some of these are probably impossible or already solved, but there are probably hundreds of other such problems which could be described. Linking up with amateur science would be a fun idea. A website or some such forum for describing problems and discussing approaches as well as setting up an amateur lab (eg building a thermocycler for $10 rather than buying one for $5000) would be fantastic.

  7. How unfortunate that most of the comments so far are pretty negative-to-neutral. Speaking as a now-professional biohacker, I can safely say that the price and investment are, while a bit painful up front, certainly not extortionate. To set up a pretty comprehensive lab in my own house, I have invested about e2000, but most starting DIYbioers wouldn’t need as much stuff to get going as I bought.

    For the naysayers, let me say that my 2k investment covered a microcentrifuge from NCBE, my own “Dremelfuge” microcentrifuge, PCR machine from, a Pearl Gel Electrophoresis rig, bunsen burner, HEPA purifier for a DIY flow hood (that works quite nicely thank-you), all my lab glassware, a variety of chemicals I’ll need for minipreps, the projected price for the handful of enzymes I’ll need for biobricking my DNA, some salts and chemicals needed for inducing bacterial competence or precipitating/washing DNA, and basic equipment like pipettes and micropipettes. In fact, I bought a lot of redundant things for experimentation that others will not need to invest in, particularly all the different DNA stains I’m testing for safety versus sensitivity.

    On top of that I buy potatoes, glucose and agar for PDA medium to feed my cells (I work with Bacillus subtilis), and I have invested a significant sum lately in the synthesis of a carefully designed DNA vector for Bacillus which I hope to test shortly (once I have obtained a license from the EPA).

    So… I’m biohacking pretty nicely without the expense that most academic labs would assume is necessary. And I say that out of experience: I worked in an academic lab for years, and I know how much they are ripped off for things that are easily substituted, DIY’d or worked around.

    Key takehome point: While academic labs have to fork out tons of money to produce highly reproducible (hence publishable) results, DIYbioers and “Biohackers” need not be so stringent provided they get the results they want. And, not to labour a point, but expedience need not come at the cost of safety; it’s very easy to run a safe lab no matter the circumstances if you stick to Biohazard 1. So far, I have been having excellent results with my garage approach, and I’m enjoying it a lot more than my “professional” work prior to this. I’d recommend it to anyone as a potential hobby if not career!

    Meredith’s work by the way is both inspired and hardly “vapourware”: it won’t be too long until it becomes doable. Based on the structure of melamine-cyanurate, the hydrogen bonding pattern of melamine strikes me as something very compatible with an RNA-based biosensor/transactivator. In fact, it strikes me that Melamine would have a stronger H-bond affinity for Thymine than Adenine, meaning a structure-interruption approach would probably allow melamine-dependent activation of reporter mRNA. It’s not easy, and it’s hardly low-hanging-fruit for DIYbio, but as an example of quality inspiration and of something tremendously powerful that will never be created by the existing system, it rocks.

      1. I have yet to apply for the license, but based on my personal conversations with the licensing office (and their encouragement to apply for a license) I don’t see any barrier to getting one that a normal lab wouldn’t have to surmount.

        For Class 1 GMOs in Ireland (That is, organisms that pose no risk to humans, animals, plants or the environment, and which are easily contained), a contained-use license costs between e125 and e250, and requires that you demonstrate that you are competent and capable of containing the GMO you create from the environment. It’s up the EPA to decide whether to license you or not.

        I’ll be making my own progress in this area public on as I go. At present, I’m just moving my lab into larger and more appropriate premises prior to submitting my application.

  8. So does this mean we’re going to have Harrison Ford going around shooting replicants soon?

  9. EarthLife Genesis By 2011 Data

    – Earth’s primal ORGANISMS are RNAs, good Sun radiation absorption-constraint, self-replicating mass formats. Corroborating evidence: life’s chirality and life’s sleep.

    – All EarthLife is evolved RNAs. All self-replicators are ORGANISMS, including genomes. DNA selected for some genomes being energetically stabler than RNA.

    – Life’s drive: RNA’s natural selection, enhance-maintain Earth’s biosphere, exploit-postpone Sun’s and Earth’s energy prior to their fueling universe expansion.

    – Drive of Life’s evolution: Natural selection is ubiquitous for ALL mass-formats/spin-arrays; must ingest energy-or-mass to
    delay-postpone eventual own reconversion to energy, all of which is destined to fuel expansion of the universe. Universe expansion reconverts singularity’s mass to energy. Eventually, as nearly all massfuel is consumed, expansion will be overcome by gravity to initiate re-empansion to singularity, reconverting ALL energy to ALL mass.

    Dov Henis
    (Comments From 22nd Century)

    Seed of Human-Chimp Genomes Diversity
    03.2010 Updated Life Manifest
    Evolution, Natural Selection, Derive From Cosmic Expansion
    Rethink Evolution/Natural Selection

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